Wow, wish our well water was that pure.
At our Arizona campus, we top off with RO treated water because the raw well water has so much junk in it from the farms around us. That has a low pH and low TA as well, and I've found that because the TA is so low, it barely affects the pool pH. In fact, I usually still have to periodically add acid as the pool pH rises from outgassing. Hopefully, it'll work out the same for you.
But yeah, get the CYA under control with drain/refill first, then run a new set of tests to start getting everything else in balance.